- AUTHOR - Heikki Lehvaslaiho
Bio::Variation::Allele - Sequence object with allele-specific attributes
$allele1 = Bio::Variation::Allele->new ( -seq => 'A', -id => 'AC00001.1', -alphabet => 'dna', -is_reference => 1 );
List of alleles describe known sequence alternatives in a variable region. Alleles are contained in Bio::Variation::VariantI complying objects. See Bio::Variation::VariantI for details.
Bio::Varation::Alleles are PrimarySeqI complying objects which can contain database cross references as specified in Bio::DBLinkContainerI interface, too.
A lot of the complexity with dealing with Allele objects are caused by null alleles; Allele objects that have zero length sequence string.
In addition describing the allele by its sequence , it possible to give describe repeat structure within the sequence. This done using methods repeat_unit (e.g. 'ca') and repeat_count (e.g. 7).
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : is_reference Usage : $obj->is_reference() Function: sets and returns boolean values. Unset values return false. Example : $obj->is_reference() Returns : boolean Args : optional true of false value
Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args :
Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : Args :
Title : repeat_unit Usage : $obj->repeat_unit('ca'); Function: Sets and returns the sequence of the repeat_unit the allele is composed of. Example : Returns : string Args : string
Title : repeat_count Usage : $obj->repeat_count(); Function: Sets and returns the number of repeat units in the allele. Example : Returns : string Args : string
Title : count Usage : $obj->count(); Function: Sets and returns the number of times this allele was observed. Example : Returns : string Args : string
Title : frequency Usage : $obj->frequency(); Function: Sets and returns the frequency of the allele in the observed population. Example : Returns : string Args : string